, and it would be great to use something
like that in place of the explicit method call above.
Best,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Jul 27, 2014, at 10:44 AM, Geert Vandeweyer
wrote:
> Hi,
>
> I'm working o
VCF:
sed -E 's/^[0-9XY]+/chr&/‘ input.vcf | sed -E 's/^MT/chrM/'
You may need to massage it depending on your platform and sed version.
Best,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Apr 20, 2014, at 11:27 AM, Sak
This is a good idea, and I’ve implemented it in this -central changeset:
https://bitbucket.org/galaxy/galaxy-central/commits/c055181847a46dc3199458d899d28d559ae43c38
If you’re working with galaxy-dist, you can pull this one changeset and use it
until the next release. Let me know if you have any
Hi Raj,
Thanks for sharing your datasets. This issue should be fixed as of this commit
in -central:
https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f42993eaa5a1fa40116d3
Best,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
Hi Will,
This should be fixed as of this commit:
https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f42993eaa5a1fa40116d3
Best,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Apr 9, 2014, at 10:03 PM, William Holtz wrote
or lines are allowed.
If you check the len file and don’t spot an issue, please send to it to me and
I’ll take a look.
Best,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Apr 10, 2014, at 2:30 AM, Aarthi Mohan wrote:
> Hi all,
>
I cloned directly from galaxy-dist:
% hg clone https://bitbucket.org/galaxy/galaxy-dist/
which gives you the latest release, and it is 2014.02.10--2–29ce93a13ac7
Best,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Mar 29, 2014, at 3:02 AM
.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Mar 27, 2014, at 4:28 AM, Shu-Yi Su wrote:
> Hi Jeremy,
>
> I reverted the files that I have changed, and also cleaned the cache once
> again. The error messages are the same:
>
&
The next step then is to revert all the changes that you pulled from -central
and report back the errors you’re seeing. Manually pulling selected change sets
can be problematic if you don’t get all the dependencies.
Best,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George
This sounds like a cache issue. Both of these scripts have been removed from
the distribution, so they should be absent from the distribution. Can you try
clearing your cache and see if that fixes the issue?
Thanks,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George
provide any
errors that you see?
Thanks,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
On Mar 24, 2014, at 11:38 AM, Shu-Yi Su wrote:
> Hi all,
>
> We have recently updated our local Galaxy installation to
> vrelease_2014.02.10--2--
; if it fails on our public server, share the
datasets with me and I'll take a look.
Thanks,
J.
--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University
On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam wrote:
> Hello,
>
> I am trying
On Jan 27, 2014, at 9:57 AM, John Chilton wrote:
> The swap over happens when
> the number of items gets sufficiently large and a jQuery-based widget
> called select2 replaces all select boxes in Galaxy - unless explicitly
> disabled. I understand the desire to disable this. I am not sure
> anyon
On which Galaxy server are you running your analyses? Using a current Galaxy
instance and Tophat v2.0.10, I wasn't able to reproduce the issue.
Thanks,
J.
--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University
On Jan 13, 2014, at 11:28 AM, &qu
Ok, then it's very likely a PATH issue. There's no magic needed here -
faToTwoBit simply needs to be on your path. It seems you've tried debugging
this already; one suggestion is to provide the full path to the executable and
see if that works.
--
Jeremy Goecks
Assi
Ok, then it's very likely a PATH issue. There's no magic needed here -
faToTwoBit simply needs to be on your path. It seems you've tried debugging
this already; one suggestion is to provide the full path to the executable and
see if that works.
--
Jeremy Goecks
Assi
Can you run the faToTwoBit tool from the command line? It can be difficult to
find the right executable for UCSC tools sometimes; if you have the wrong
executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not
found' error.
--
Jeremy Goecks
Assistant Professor
Can you run the faToTwoBit tool from the command line? It can be difficult to
find the right executable for UCSC tools sometimes; if you have the wrong
executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not
found' error.
Best,
J.
On Jan 3, 2014, at 11:35 AM, Jasper Jan Koeh
wrong? I also
> don’t see any error messages in the log above.
>
> Thanks and regards,
>
>
> Pieter.
>
>
> From: galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Jeremy Goecks
> Sent: dinsdag 11 juni 2013 19:06
> To: Edlun
>
> Thank you again for the help….without this piece of useful information, i
> might had spent days and days on this : )
>
> Best regards,
> Shu-Yi
>
> On Nov 22, 2013, at 2:40 AM, Jeremy Goecks wrote:
>
>> This appears to be an issue with the dataset that you&#
> Without details about your incoming data rate and size, it's very difficult
> to answer this question. I suggest taking some of your data, running it on
> our public server (usegalaxy.org), and seeing how long it takes. RNA-seq
> tools (Tophat, Cufflinks, etc.) use 4 cores for a job, so you c
Do you see any errors in the JavaScript console? Does this only happen on
particular Web browsers?
J.
On Nov 15, 2013, at 10:15 AM, Yec'han Laizet wrote:
> Hi,
>
> In the current version of galaxy stable branch (5c789ab4144a), the tool panel
> is empty when installed (freshly and out of the
Without details about your incoming data rate and size, it's very difficult to
answer this question. I suggest taking some of your data, running it on our
public server (usegalaxy.org), and seeing how long it takes. RNA-seq tools
(Tophat, Cufflinks, etc.) use 4 cores for a job, so you can estima
> Why are Custom Builds only enabled if you're *not* using remote_user ?
> Is this because they're related to user preferences (as per the code in
> lib/galaxy/webapps/galaxy/controllers/user.py)?
This may be an artifact of a time when user preferences were immutable. Do
Custom Builds and Prefere
no errors in the console.
>
> Thanks, Thomas
>
> Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
> Gesendet: Dienstag, 22. Oktober 2013 15:55
> An: Berner, Thomas
> Cc: galaxy-dev@lists.bx.psu.edu
> Betreff: Re: [galaxy-dev] trackster: missing graphs for large number of
A couple questions:
(a) are you using a custom build? If so, does the build show the correct number
of chromosomes?
(b) do you see any errors in the JavaScript console when trying to view the BAM
file?
Thanks,
J.
On Oct 21, 2013, at 11:05 AM, "Berner, Thomas"
wrote:
> Hey guys,
>
> we wan
For your workflow, try going to 'Share or Publish' option --> and share via URL
(and publish it if you want). The workflow can then be shared with a large
number of people using the URL.
Best,
J.
On Oct 21, 2013, at 4:07 AM, Anatoliy Pandorin wrote:
> For a long time I used release_2013.01.13
This issue was fixed in this changeset:
https://bitbucket.org/galaxy/galaxy-central/commits/8c663e656f64a60dac55979841947e78ce23a473
If you update your Galaxy to the revision on galaxy-dist this problem should go
away.
Best,
J.
On Oct 18, 2013, at 1:10 PM, lardo wrote:
> I run a local instan
You'll need to do two things:
(1) Install wigToBigWig and bedtools; see steps 2 and 3 here:
http://wiki.galaxyproject.org/Visualization%20Setup
(2) Update your datatypes_conf.xml file:
If you haven't made changes to your datatypes_conf.xml file, you can just copy
datatypes_conf.xml.sample to d
I'm still not fully understanding your usage scenario.
> A simple example is the creation of a full history based log file.
I imagine that this would be an ideal use of the history API. Rather than
having tools log history, write a script that uses the API to generate a
history log.
> My more
Thanks for reporting this issue and workaround Ulf. I've committed a fix that
addresses this issue by only includeing the -split option for BED/GFF/GTF
datasets and not VCF:
https://bitbucket.org/galaxy/galaxy-central/commits/b8d8f81bed872e58b4691643de8a08fa41662e71
Best,
J.
On Sep 12, 2013, a
id resolution
> architecture. Happy to talk on the phone if that would be a better use of
> your time.
>
> Thanks,
> Curtis
>
>
>
> From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
> Sent: Wednesday, September 25, 2013 8:43 AM
> To: Curtis Hendrickson (Ca
sted in tool_conf).
> There was no version pull down to get the 0.0.6 version.,
>
> Any idea what I’ve missed?
>
> Regards,
> Curtis
>
>
> From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
> Sent: Thursday, September 19, 2013 3:17 PM
> To: Curtis Hendri
> At line ~694:
> incoming['__user_name__'] = user_name
> + if job.history and job.history.id:
> + incoming['__history_id__'] = job.history.id
> + else:
> + incoming['__history_id__'] = 'unknown'
> I have tested this change and it appears to give me exactly w
> We can hack the old wrapper back in, using a hard-coded path to the old
> cuffdiff.
You could also use Managed Tool Dependencies for multiple versions of cuffdiff:
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
> Shantanu suggests it might be a better world if we create a tool
> I know the general versioning problem is address through the tool-shed
> mechanism, but for the remaining core wrappers, can maintainersplease update
> wrapper version numbers when making changes?
Not bumping wrapper versions is an oversight, not deliberate.
>
> For this wrapper set, how wo
> hi Jeremy,
> in the histories controller, I could find no example to nicely obtain the PUT
> and POST content payload. Am I missing it?
> So I think a bad answer to my question is the following code. But I really
> don't like my _get_payload() hack reaching into the trans.environ object.
:
> Hey Galaxy,
>
> I am trying to use CuffDIff with replicate analysis on a local instance. I
> saw that Jeremy Goecks had a solution to this problem:
> http://user.list.galaxyproject.org/Cuffdiff-changes-tt4655893.html#a4655901.
> Could I see/use this source code please? I
Take a look at the histories controller (histories.py) for an example +
documentation on how Galaxy realizes a RESTful interface. In short, you'll want
to implement different methods for create, read, update, and delete. Kwds are
miscellaneous parameters included in a request that are not explic
You're not missing anything; using validators is the right way for checking
parameter values. However, the page refreshes + validation errors is certainly
less than ideal for usability. We're in the process of transitioning tool forms
to a JavaScript-based framework so that full page refreshes (
This isn't an easy question to answer. Here's why:
*there is significant variation in mammalian genome size; of course, larger
genomes require more resources, but the relationship is difficult to quantify;
*assembly can take anywhere from a day to a week depending on software and
resource choice
> STAR aligner
I have a partial STAR wrapper that may be useful:
https://bitbucket.org/jgoecks/jeremys-code/src/d7096c132657420f08b540c6954b947f648aac80/galaxy/tool-wrappers/star.xml?at=default
Whether you use this code or not, I do have one request: please put the output
in BAM rather than SA
> My attempts to visualise a vcf file in trackster fail. I can visualise
> the corresponding SAM/BAM files fine. I can visualise the same file on
> Galaxy main too, but not in my local install.
To be clear, you can visualize the VCF dataaset on main but not locally? Can
you visualize SAM/BAM da
There is currently no simple way to circumvent this behavior. If you want to
modify the code, take a look at display_data() in data.py -- you'll want to
bump up the max_peek_size (line 351 in -central) above 10 MB for HTML datasets.
Good luck,
J.
On Sep 9, 2013, at 6:16 AM, Gromobir wrote:
> H
> Dear all,
> in one of my tools I'm populating a list of possible
> choices from a file in the history using the from_dataset> tag.
> Now using the tool as part of a workflow, the choices are
> not calculated at the setup stage, but I have to enter
> free-text and Galaxy seems to evaluate whethe
> Is it currently possible to export histories via the API?
Not possible yet but is definitely something we'd like to implement and/or see
from a community contribution.
Best,
J.
___
Please keep all replies on the list by using "reply all"
I suspect there is an issue with Trackster when changing from one mode to
another. Can you confirm that by saving and refreshing the visualization, you
can view the dataset in different modes?
Thanks,
J.
On Sep 5, 2013, at 4:06 AM, Joachim Jacob | VIB | wrote:
> Update: the 'dense' option does
Please take a look at this page for setting up visualizations:
http://wiki.galaxyproject.org/Visualization%20Setup
Let us know if you have any questions.
Best,
J.
On Sep 1, 2013, at 9:37 PM, shenwiyn wrote:
> Hi ,
> I found that the visualization of Circos works greatly in Galaxy main,but
> f
>
> Question: How save is the optional attribute ? I mean how consequent are
> you in this matter when the tool definition xml is to be created.
It's not clear to me what you're asking. That said, it's important to
distinguish between Galaxy tool wrappers and their corresponding tools. Either
d
>>
>> There are sporadic reports of this issue, but I haven't been able to
>> reproduce it. My best guess is that it's due to trying to use the custom
>> build before Galaxy has finished creating it. To ensure that the custom
>> build is ready for use, make sure to wait for Galaxy to show the n
As you discovered, this isn't possible yet. You'll need to break up your
parameters into multiple conditions, so Yes/No for Blast and Yes/No for Fasta.
Best,
J.
On Aug 26, 2013, at 6:33 AM, Kahlke Tim wrote:
> Hei,
>
> Is it possible to use a for a conditional? I'm
> trying to use it for che
It appears you are missing some updates. This issue was fixed in this changeset
9992:
--
changeset: 9992:7105c53139d4
branch: stable
parent: 9990:f35c0441e374
user:jeremy goecks
date:Tue Jun 11 17:34:26 2013 -0400
files: lib/galaxy/tools/actions/__init__.py
>>
>> Am I missing a converter?
Yes, you are missing the bed_to_bigwig converter.
If you haven't made changes to your datatypes_conf.xml file, you can just copy
datatypes_conf.xml.sample to datatypes_conf.xml to get the needed converters.
If you've made changes to datatypes_conf.xml, you'll
This isn't possible right now, but could be added without too much difficulty.
Take a look at the method Job.prepare in lib/galaxy/jobs/__init__.py - you'd
want to add the job id to incoming or param_dict variables.
Also note that Galaxy already has links between datasets and jobs in its
databa
>
> Internal Server Error
> Galaxy was unable to sucessfully complete your request
>
> URL: http://127.0.0.1:8081/user/dbkeys
> Module galaxy.web.framework.middleware.error:149 in __call__
>>> app_iter = self.application(environ, sr_checker)
> Module paste.recursive:84 in __call__
>>> return self
This question is best directed to the galaxy-dev mailing list because it
concerns developing around Galaxy, so I've moved it there.
> However, if I understand it right, the idea of the XML tool config is to
> provide a description of the galaxy graphical user interface rather then a
> general d
> If I share a history, it produces a url with the datasets. This is good. But
> if you click on the eyeball in this view, it shows the dataset in its raw
> form. Its as if the code path does not go through the sophisticated datatype
> logic. Is this deliberate or an oversight?
Incomplete inte
This bug has been fixed in our code repository and will be included in our next
release, which is due out in a couple weeks.
Best,
J.
On Aug 1, 2013, at 1:25 AM, Philipe Moncuquet wrote:
> Hi guys,
>
> Since the last update of Galaxy. We are enable to edit pages on our local
> instance. Pages
Yes, this works on my local instance. Did you restart your Galaxy instance
after adding the welcome_url setting?
On Jul 29, 2013, at 11:02 PM, wrote:
> Yes I tried that but I still only see the default welcome.html page. Have you
> got this to work?
> Thanks
> Neil
>
> F
*context.local_conf)
> File
> "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py",
> line 57, in fix_call
> val = callable(*args, **kw)
> TypeError: make_prefix_middleware() got an unexpected keyword argument
>
There's an undocumented setting in the universe config, welcome_url, that can
be used; if you point this as follows it will bring up the upload tool.
welcome_url = /tool_runner?tool_id=upload1
On Jul 29, 2013, at 3:28 AM, Ross wrote:
> Neil,
> good news: the initial center panel renders static/
> The file that Gift is producing is already an html file and there's
> already an html datatype in Galaxy by default. The output file in
> question just invokes remote javascript libraries inside
You'll want to use composite datatypes:
http://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes
On Jul 24, 2013, at 3:08 AM, Pankaj Narang wrote:
> Dear Developers,
>
> I want to design a tool whose input is folder containing files and
> sub-folders.
> I was wandering which value s
It would be very useful to know what's in the 62kb file -- is it a BAM file or
a long error message?
Also, the Bowtie2 wrapper has been updated in -central, so you may want to
check that out as well.
J.
On Jul 24, 2013, at 5:07 PM, Maddhi, Srinivas wrote:
> [Copying the list].
>
>
> -Or
Fastq datasets can have many different encodings for quality scores. See here
for details:
http://en.wikipedia.org/wiki/FASTQ_format
Many tools in Galaxy require that fastq datasets be in fastqsanger format and
designated as such in its datatype. Because your data appears to be in
Sanger/Illum
What you envision probably isn't possible yet.
Two ideas for extending Galaxy:
(1) use the "show structure" functionality from the history menu to generate a
summary page
or
(2) create a Pages API and implement a function to create and save a new page
that describes the structure.
Best,
J.
This is a known issue that we have plans to fix. You can follow our progress
here:
https://trello.com/c/JfB2w1Br
Best,
J.
On Jul 12, 2013, at 6:09 AM, Mathieu Bahin wrote:
> Hi all,
>
> We have a Galaxy instance that we are regularly keeping up to date following
> the Galaxy main, so we have
> bedtools genomecov -bg -split -i stdin -g
> /usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len
>
> However this crashes. After looking in my computer, I find that bedtools do
> not contain the file genomecov. Is this an erroneous assumption of mine or
> have I installed some
The toolshed has a wrapper for cummerbund:
http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund
On Jul 12, 2013, at 12:03 AM, sridhar srinivasan wrote:
>
> Dear Developers,
>
> Could you please tell me the possibilities of using the R package cummeRband
> for visualization of RNA-seq data i
Here's a cloud image that the Galaxy team often uses for workshops:
http://wiki.galaxyproject.org/CloudWorkshop
Good luck,
J.
On Jul 11, 2013, at 1:28 PM, Maddhi, Srinivas wrote:
> Hi Max,
>
>
> An alternative approach, in case that becomes necessary, would be to set
> up your own temporary i
You have two options:
(1) set the number of workers in the LocalJobRunner;
(2) Galaxy can use many different computing clusters, all of which have queuing
systems that you can control.
See this page for more details on both options:
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluste
You'll need to make sure that bedtools is in your Galaxy user's path.
Best,
J.
On Jul 9, 2013, at 6:40 PM, Perez, Ricardo wrote:
> Dear all,
>
> As I was trying to do visualize my data set in trackster, I get the following
> error:
>
> /bin/sh: 1: bedtools: not found
> sort: fflush failed: st
Dbkey specifies the base assembly; unique build ID species the particular
assembly. This is most often used for human assemblies: dbkey is hg19 and build
ID might specify some combinations of autosomes, sex chromosomes, and
mitichondrial DNA.
J.
On Jul 6, 2013, at 6:16 PM, Perez, Ricardo wrote
> That's certainly neater. There are many more wrapper that do the same - using
> mkdtemp() without a dir argument. Is there any plan to perform the same
> changes on these (bam-to-sam, etc...)?
I made the same change for the BAM to SAM wrapper so that it create temp files
in the job working di
In the spirit of this solution, I've implemented something similar in -central
changeset:
https://bitbucket.org/galaxy/galaxy-central/commits/c7a07f350887fe3b4e822ba6b26b63ac3ac14bdf
The tool now creates temporary files in its working directory, which can be
configured via the 'job_working_dire
> To follow up on that, I thought it would be useful to have that mentioned in
> the wiki. I did some modifications to indicate the necessary changes to be
> done to universe_wgi.ini file
> (http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles). I
> hope that is OK.
>
> Besi
> Can anyone comment on this? Why insert a weird non-user friendly WYM stamp
> guid?
Just unfinished functionality. It's fixed in -central changeset 2cabbf368763
and will be available on our public server in a couple weeks.
Best,
J.
You'll need to update the settings in your universe_wgi.ini file (and restart
Galaxy) to get these options to show up; specifically, take a look at
'library_import_dir' and 'allow_library_path_paste'
Best,
J.
On Jun 28, 2013, at 2:22 AM, Lionel Guy wrote:
> Hi!
>
> I'm trying to upload multip
>
> To have Trackster visualization working properly in Galaxy, one needs
> bedtools.
> Yet in our instance (running under Ubuntu OS), installing bedtools in the
> galaxy home directory and setting the environmental variable PATH in the
> .profile file so that it includes the path to ~/bin/bedt
> I was looking at galaxy/dist/tools/sr_mapping/bowtie2_wrapper.* and it
> does not seem to challenging to add another field where a user could
> specify some integer value that we simply pass to the the
> tag in the xml file.
>
> Would this be the correct way to go about this?
Yes, this is corr
> "A converted for this file is not installed. Please heck your
> datatypes_conf.xml file."
>
> How exactly do I find out which converted files I am missing?
This information isn't easy to find yet, so I've created a card for it:
https://trello.com/c/E3ReiSVU
If you haven't modified your dat
dwgsim (and dwgsimeval) may be useful to you:
http://toolshed.g2.bx.psu.edu/view/nilshomer/dwgsim
http://toolshed.g2.bx.psu.edu/view/nilshomer/dwgsim_eval
Good luck,
J.
On Jun 24, 2013, at 11:47 PM, מירב . wrote:
> Hi,
>
> I want to do some checks on tools I'm using(in this case I'm checking
>
> Error running cuffdiff. [12:48:21] Loading reference annotation.
> Warning: No conditions are replicated, switching to 'blind' dispersion method
> [12:48:33] Inspecting maps and determining fragment length distributions.
> terminate called after throwing an instance of
> 'boost::exception_deta
Here's some specific information about what the PATH variable is for UNIX
systems and how to set it: http://kb.iu.edu/data/acar.html
Many folks do the following so that you only need to add a single directory to
your path:
(a) install all tools in one directory;
(b) create a "bin" directory in
Take a look at the item_tags API controller; you can manage (add/delete/show)
history, dataset, and workflow tags using it. There's not much documentation
for it yet, but it should be pretty straight-forward. Let us know if you have
questions.
Best,
J.
On Jun 20, 2013, at 9:59 AM, Philip Mabon
The .dat file *is* the dataset file, so you can use it directly with your tool.
J.
On Jun 20, 2013, at 2:52 PM, vijayalakshmi wrote:
> Hi all,
>
> I have written a java tool to which I have to pass an existing file's name.
> In the XML wrapper, I am choosing the file from the history using
You'll need to (a) add an output file to your tool configuration ( see
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coutputs.3E_tag_set
) and (b) write your output to the file. See other tool wrappers (e.g.
/tools/filters/cutWrapper.xml) for an example.
Good luck,
J.
On Jun 14
Elwood,
It's not clear what steps you're having problems with, so it's difficult to
offer help. Here's the outline that I use to RNA-seq running with Galaxy:
*download Samtools, Bowtie2, Tophat2, and the Cufflinks tool suite and add them
to my galaxy user's path;
*download the iGenomes data pac
You'll need to wait until the history is ready for download -- i.e., Galaxy
provides a .gz file rather than a Webpage at that URL -- before using wget.
Galaxy returns a webpage (text/html) while preparing the history for download;
this is likely what you are downloading now.
Good luck,
J.
On
> Hello,
> After the latest update of Galaxy I saw that the cuffdiff wrapper is for
> version 2.0. I updated the $PATH to cuffdiff v. 2.0.2 but when I run cuffdiff
> in Galaxy I get the following error:
> Error running cuffdiff. cuffdiff: /lib64/libz.so.1: no version information
> available (re
> My use case involves working with a lot of histories, and I need to
> jump back and forth between them fairly frequently. However, it's a
> bit inconvenient to have to click on the "Options" button on the
> rightmost pane, "Saved Histories" in the drop-down menu, and select my
> history on the ma
>> Trackster displays an error after opening a saved view:
>>
>> ***
>> Error: The requested genome file
>> (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be
>> opened. Exiting!
>> sort: write failed: standard output: Broken pipe
>> sort: write error
Anna,
Try following these steps:
(1) Make your history accessible (Share or Publish --> Make History Accessible
by Link).
(2) Export your history again; make sure to wait until you can use the URL to
download a .gz file of your history.
(3) Try importing it via URL to the Huttenhower Lab Galaxy
Hi Linda,
1- Should the "Set display mode" give out different output?Not yet. VCF visualization is new to Galaxy, and mode switching isn't implemented yet. (It will be implemented in the next release.) What you're seeing is the display of individual variants; of course, trying to view so many varia
> I want to select a date from a calender in my tool, but I think that it's not
> possible in the xml.
Correct, date inputs are not currently implemented in Galaxy parameters.
> Is this possible? With javascript? Or what?
It's possible if you want to extend Galaxy a bit. I suggest (a) adding a
>
> how to get the mapping summary from bowtie2 using galaxy interface..
This isn't possible right now, but I've filed a Trello card that you can follow
to watch progress on this enhancement:
https://trello.com/c/yFeXvhUg
Of course, a patch/contribution addressing this issue would be fantastic
I tracked down this issue to a bug in the workflow export code, and I've fixed
it. The fix will appear on our public server early next week; please let us
know if you're still seeing this error late next week.
Best,
J.
On May 23, 2013, at 9:50 AM, Andreas Kuntzagk wrote:
> For the first of th
When a user creates an account, s/he can create/copy/delete histories and copy
datasets from history to history to organize data. Each history, then, is a
like a library folder.
Best,
J.
On May 29, 2013, at 11:02 AM, 吳正華 wrote:
> Hi, galaxy community:
>
> I’ve set up a local galaxy for our i
These are options we'd like to add to Cufflinks, and I've created a Trello card
for this enhancement:
https://trello.com/c/U7nceKdj
I want to add that community contributions via patch or pull request are highly
encouraged and are likely to be quicker than waiting for the core team to get
to t
> Hello!
> I am trying to enable Trackster on our local galaxy to
> visualize the mapping results.
> But, so far, it is not working.
> Is the twobit.loc file necessary for using Trackster? or is it just optional?
>
> Best regards,
> Menorca
Twobit files, configured via twobit.loc, are optional.
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